Whatever remains,no matter how improbable,must be the truth
by 221BWholockedfandomsMaddie
Summary: John Watson is happy, being normal. He is getting married to Mary Morstan. It's been 3 years since the fall, and Sherlock Holmes comes back into his life again, a chaotic, slightly unstable, more vulnerable man than before. Normalcy is a fragile thing and what happens when it gets broken-again? Johnlock eventually. Rated T to be safe.
1. Chapter 1

**Sorry if John seems a little OOC,its just that I really have no idea how he will act in season 3, and I don't know very much about Mary Morstan other than what is in the original ACD canon. **

London. It had been almost 3 years since he had seen it last. Hunting down Moriarty's web, his spider's web of twists and turns and false leads-had taken longer than he had thought. But it had been worth it for John. He wondered what John would say to him-if anything. He knew that it was of course not a socially polite thing to do, fake your own death for three years. He knew that life would probably never be the same again, how could it be? Normalcy has become a foreign concept almost. Prague, Paris, New York, Tokyo, New Delhi,Los Angles and many more, places that further lead to the opaque, untwisting of the web. Now there was only one link left to destroy. Sebastian Moran,Moriaty's right hand man and master sniper. He had evaded him long past the rest. Sherlock wanted to get it over with however he knew he couldn't let his emotions take over his thoughts. He had cried for John once, when he was in the morgue silent tears that flowed salty on his face. He had felt so guilty then, and he was guilty now the bitter, metallic taste of it in his mouth. Did guilt really have a taste? he thought. Remorse,guilt,he was a different man than the man he was 3 years ago he was more vulnerable.

_"And I behold London, a Human awful wonder of God"_

John was back to normal life. Almost anyway. After 3 years, he still had nightmares: Sherlock falling and him screaming his name replayed again and again and it was always the same. For months afterward, he would hardly do anything. Just sat there. Didn't eat, didn't sleep, didn't go out much. He moved back to his small, brown and tan army pension apartment. He only went back to 221B once, he was afraid so afraid. There are 5 stages of grief. He was a doctor he knew this, had went through this before. Denial,Anger,Bargaining,Depression,and Acceptance. Then he had met Mary. He found that he could laugh again. He was okay. Okay was good. It was peaceful, it was the not having to worry if your flat mate had set the flat on fire and that was okay. It was the not having to worry that your flat mate would relapse into past habits. It was the not having to worry that you would get abducted by Moriarty. It was normal. He had finally accepted Sherlock's death but it still affected him.

`- "More wine sir?'' The waiter was back,John thought. The waiter had been peskily coming back to the table every 5 minutes or so and it was getting annoying. Very annoying actually because here he was having a nice romantic dinner with his fiancée , Mary Morstan.

''No, no thank you" John snapped. The waiter left in a hurry, carrying champagne to some other unfortunate's table. John's eyes followed the waiter as he made his way back to where ever he had come from, at least until he turned the corner and he couldn't see him any more.

"-and I think we should start making plans for the wedding, you know putting together guest lists and the like, John are you listening to me? You look like you zoned out there for a while" Mary's words cutting into his thoughts. He realized he hadn't been listening to her and didn't quite catch the first part of what she said.

He turned his head back towards her, blinking. "Sorry Mary, I was just thinking. What's this about the wedding? We have five months to plan you know" He was constantly worrying about this fact because they should in fact, get a start on it.

She looked at him quizzically."What were you thinking about?"

He only realized then what exactly he had been thinking about. Sherlock, and the time when they took the Hound of the Baskervilles case, and Sherlock had given him poisoned tea,he did this, when he saw or heard something that reminded him of his dead flat mate, he kind of zoned out. But that was normal grief he told himself, people always do that when people they know die.

He set his jaw. Shut up he told himself, it does no good to wish Sherlock wasn't dead. It was what it was and that was the cold hard truth of it. "Nothing, I was thinking about nothing'' He said, casually as he could.

She rolled her eyes. "Come 'on I know you better than that John, what were you thinking about?" He could see the small glimmer of worry in her eyes. She knew what he went through after Sherlock fell. Didn't want to see him fall back into that. He was better he told himself now, even with his limp back.

"Mary...trust me I wasn't thinking about anything important" he said. Lies, and he knew it. Why was he suddenly thinking about Sherlock so much? He hadn't thought of him this much in a while. He was always at the back of his mind, but most times, stayed there.

He picked up his champagne flute and took another drink.

"Okay, okay I'll drop the subject" She retorted.

They moved on and were talking about his work, and a client who had been there earlier that week who had a fractured skull and a broken arm.

What they didn't see,because they do not see or observe, was at that moment, a familiar ex-consulting detective was watching them. He was standing in the shadows by the restaurant door, hoping not to be seen. He had been in the area and thought, why not? It had been three years after all and he wanted to see John. He wanted to see him one last time because he was going to go corner Sebastian Moran soon,(he didn't know exactly when, he had to find a weak spot in Sebastian's armor first). He observed that John's limp was back, he had a moustache and was almost un recognizable as the great man he had been 3 years prior. He seemed to treat the woman with respect-hmm sentiment? Yes, engagement ring on lady's finger. Well, that was good he supposed, it meant he had most likely gotten over his "death". But he couldn't help but feeling a sight bit...he didn't know exactly what. He was afraid to put a name to it.

John suddenly shifted his gaze, just a bit and looked over Mary's shoulder, towards the door. He felt like he was being watched.  
He looked up and met the gaze of a familiar,dark-haired figure. A figure that should be dead.

**Authors Note: This is going to have more chapters, and I'm thinking I'll update on Friday, because I have exams all this week and I won't get around to it. Please read and review please! **


	2. Chapter 2

_Because I can't forget _

_ Back and forth through my mind _

_Behind a cigarette _

_And the message coming from my eyes _

_ Says leave it alone _

_ Don't want to hear about it _

_ Every single one's got a story to tell_

John froze. I must be going crazy he thought, Sherlock is dead. But no, he was still there, half hidden in the shadows. He shook his head. It's nothing, perhaps its just a guy that looks like Sherlock. Nothing to worry about, not really. He averted his gaze back to Mary. But a seed of doubt had planted itself in his mind. "Did you see someone you knew? You went very pale there for a second...are you feeling alright? You have been acting a bit odd this whole evening, what's wrong?'' Mary asked him gently.

John pinched the bridge of his nose. "I thought I saw an old friend of mine, from years ago...but I don't think it was him." He grimaced as his voice wavered. He hoped she wouldn't notice the underlying unbelief in his voice.

She narrowed her eyes. "I don't believe you."

''Why not?" "Because why would it make you pale like that? It looked like you saw a ghost" Her tone has clipped. Ha. If only she knew how close she was to the truth. But no, Sherlock was dead. He was seeing things, yes that was it. However, he couldn't shake the image of the dark-haired detective from his mind.

He sighed. "I did not see a ghost, no its just that this certain friend, well I haven't seen him in a long time. Thought he wasn't living in London anymore" That's true he thought, so it's not really a lie. He didn't like lying to Mary; tried to avoid it if anything.

The waiter came back and told them that they were free to go because they had paid for their meal a few minutes earlier.

As he cleared the table, she sighed. "Fine fine keep your secrets!" She teased

"Hey,I'm going to go get some air, I'll be back in 5 minutes,probably not even. I'm just...a bit shaken up,alright?"

She raised a brow. "Okay?"

He stood up from the table and walked to the door and pushed it open. It closed behind him with a soft click. The streets of London were dark at this time of night, as it late. There was a lot of traffic on this street, everyone racing and scurrying to get to wherever they where going. John liked London at night, lit by city lights. You had never experienced life if you didn't chase a few criminals through the streets he thought wryly.

It was only then that he saw who was leaning up against the building wall on the opposite side of the street. There weren't any shadows to hide him there, as the street light cast a harsh glare against that side of the building. Sherlock Holmes. He froze were he stood. Ghosts didn't have shadows did they? No don't be ridiculous. Ghosts don't exist, no be rational he told himself,yeah but I saw him fall. He's dead-but is he really? he asked himself, that seed of doubt growing into a sapling.

- Sherlock Holmes was in fact, leaning up against a wall, observing John with faint amusement. He wondered if John thought himself still sane. Probably not, he decided. John thought he was-had been dead for the past 3 years. He very clearly did not need this kind of emotional disturbance in his life. Don't think Sherlock didn't care because he did. He just wanted to speak to John again. Again, before he fought Sebastian Moran. Because he could die. Actually die this time. He had been lucky when unraveling Moriarty's web which was good of course, it didn't mean he didn't get shot a few times, but luck was on his side.

"Hello John"

John's face paled. He knew that voice-the voice of his dead best friend.

"I'm actually here John. You're not seeing things."

John's eyes narrowed. "You're dead I saw you jump" His voice cracked as he said it.

"John, just because you see does not mean you observe-not really. I faked my own death. And it had to be clever enough-close enough to actually dying so that you would believe it."

John approached him.

"Why? Why did you fake your own death Sherlock, and leave me to believe you were dead and then you come back 3 years later?!" He was yelling now, he was angry very angry. As he had right to be.

Should he tell him or should he not? Seconds are strange things, they are such minuscule measurement on the time scale, but they can pass so slowly, and when your making a decision it makes them go slower. But they always pass because life, like many things always moves forward-usually. And isn't it strange really that a single decision made in such small time allowance can have such an interesting outcome on your life? Or it could be a bad outcome. Either way, you only get a few seconds. After that, well time tends to run out.

"I can't tell you John, not now. I can't tell anyone. Not yet. But I will tell you that it was a life or death Moriarty shot himself in the head. _He had a fail safe, and it was himself." _

- John brought his arm up and swung. You could hear the impact of bone hitting bone. And then he swung again-just for good measure because I mean really? If he would've let himself he would've most likely half killed Sherlock but something held him back. Sherlock would have a black eye and a sore, almost fractured jaw for a while and he didn't care one damn bit.

He pulled his arm back and inspected his knuckles. They were bloody, rivets of red running down his hand. He didn't know if the blood was his or Sherlock's. He didn't care. He was feeling very, very pissed off. He then turned around and walked away. He could feel the anger rippling through him, almost threatening to destroy.

Mary was waiting at the table inside looking impatient. She smiled when she saw him come through door, but her smile faltered and fell when she saw him looking slightly disheveled and his bloody hand.

"What happened?!" "I got in a bit of a fight with that old friend of mine." John said angrily.

They got up and were just outside when John looked at the place where Sherlock had been before. He was gone thankfully. Anyway...They were waiting for a cab when...

"Who was it? Your friend that you got into a fight with, who was it?" She asked quietly.

He clenched his teeth. "Oh I'm sure you could guess Mary'' His voice cool and controlled.

"I-I don't know John, who?" The traffic and noise of the city at night drowned out his response. The cabs and other cars rolled on by. A cab stopped by them and they got in. " North Agere Street please"

"So honestly John, what old friend did you run into?'' He stretched his knuckles, seeing that the crimson rivers were not running anymore. It hurt like all get out though, but he could deal with that.

"This is going to sound insane it really bloody is, but I promise you I am not insane. The old friend that I ran into was Sherlock Holmes."

She put her hand on his shoulder,"John, Sherlock's well...he's dead".

He raised his head. "And I should be the one that should know that best of all shouldn't I?"

"I didn't mean- " Of course you didn't mean, Mary but its true" He said cutting her off.

"I'm sorry. I just. It's impossible!"

"Not impossible, just improbable. Apparently he faked his own death, if that is a thing that can be done when you jump off a damned building!"

"John, he probably did it for a reason, I mean to jump off a building and going through the bother of faking your own death, I imagine it would be a hassle, and then just disappear for 3 years? No, he did it for a purpose"

"Well whatever that purpose is, it certainly isn't very clear at the moment" He said angrily.

John got back to his flat and left Mary to go to hers on the other side of town. They didn't live with each other yet because their jobs were on opposite ends of the city and they didn't want to move yet, and it's not like they were actually married. Yet. -

Later that night he went over things in his mind. "I can't tell you John, not now. I can't tell anyone. Not yet. But I will tell you that it was a life or death matter. James Moriarty shot himself in the head. He had a fail safe, and it was himself." What did Sherlock mean by that? So he couldn't tell anyone,and if he hadn't jumped off the building he would've died, so he took the chance and faked his own death? But to what motivation? Why did he jump and stay dead? The scandal perhaps. The thought that everyone thought Sherlock Holmes was a lair and a fake...but he wasn't was he? He had trusted Sherlock Holmes with his life a few times, and he was still alive. But it was the fact that he had been gone for 3 years and hadn't told anyone much less John that made him be untrustful. And why had he come back now? A million questions flew around his head. And he didn't know the exact answer to about 999 of them. He knew Sherlock had faked his death and that was it. And then, he realized.

_"He had a fail safe, and it was himself". _

**Please review/follow! So I did get this done about two days early,but as I said,I have exams so I'm going to be busy. Do you think I portrayed John well? I mean,he's not going to just let Sherlock back in his life is he? Of course not. :P **


	3. Chapter 3

**Okay, I know I haven't updated in forever, and Season 3 is in 6 days, and I'm really sorry. Anyway-here it is. Chapter 3. I don't know if/or I will update again. But I probably will. Enjoy! :) **

_Tell me your secrets and ask me your questions_

_ Oh, let's go back to the start _

_ Running in circles, coming up tails_

_ Heads on a science apart_

_Nobody said it was easy _

_ It's such a shame for us to part _

_ Nobody said it was easy _

_ No one ever said it would be this hard_

_ Oh, take me back to the start_

There was a knock on the door. Which was strange, he thought. No one but Molly knew were he was-and she was working. After all, he had only just gotten back to London in the last few days. Probably was a mistaken address but you couldn't be sure. He un steeped his hands and walked to the door quietly. A piece of paper had been slid under it,a simple small white piece of tackboard. He picked it up and looked at it." Sherlock Holmes" was written in a neat hand. He flipped it over.

- E -H A

A cypher. Hmmm. He mentally went through all the cyphers that he knew of that would apply...It couldn't be that simple, could it?

Let's say the message used the alphabet code-you know 1=a,2=b,3=c,and so on and so on. So:

AGCB - E- HA = 17 32 5 81

And then,since there is no letter that is equal to zero in the alphabet, let's say that Sherlock figured out that the "-"'s were 0's. Simple-child's play almost. Now the numbers looked like this:

17 320 5081

What could this mean? It could mean anything. Wait-there were 3 distinct groupings of numbers... but something was missing. A decimal place:

1.7 320 5081

Now the numbers looked like that. But what had the Sq. Root of 3 had to do with anything? The numbers couldn't be atomic numbers or of the elements. What about a street address?

1.7 320 5081

He grabbed a book from a self. The London A-Z. He started flipping through it and finally found it. 5081st street. He shut the book and went over to his computer and typed in "5081st Street, London". He found that there were lots of warehouses on that street-a little out-of-the-way side street on the very fringe of London. One of the warehouses was entitled "warehouse 320" and it was on 5081st street-and after a while of looking saw that the warehouse had 20 units in it.

Unit 17 Warehouse 320,Street Address 5081,London

His phone was in his coat pocket, which was hanging by the door. He got it and looked through his recent texts-1 from an anonymous number.

**I'm waiting. You know were to go. The game is afoot.-SM**

He liked the clever ones. They were so brilliant, so desperate not to be caught but yet wanting to show the world exactly what they could do. And, rather like the cabbie in "_A Study in Pink_", sometimes their own cleverness was their own undoing. They were the ones also, he thought, that made the game into a risk, and they played bluffs and triple bluffs, and so on. All for the thrill of the game, the adrenaline pumping through your veins.. He was still the addict, he thought ruefully. But he didn't play it as much of a game anymore. He had played the risk and he had so-called sacrificed himself for risk. The game was still afoot, but there were people to be taken into consideration.

He got out of the cab into the dark side street. There wasn't any traffic on this street, and there weren't any houses so the darkness folded in on everything, but the city never got that dark, so it was dimly illuminated. Sherlock walked to the singular warehouse that was at the end of the street, which boldly stated "Warehouse 320" on a metal plate. The door was opened slighty,creaking in the doorway. Someone, or something had been here recently. He reached for the door and swung it open, stepping into the gloom. He saw that he was in a high ceiled room, divided into smaller rooms units he supposed. He passed a few: 1,2,3,4,5 etc. He didn't know how many units were on a single floor, but judging as since there was two floors, unit 17 was most logically upstairs.

He went up the stairs, creaky and old but metal-they seemed to go on forever-and again time is a funny thing isn't it? He emerged in the rooms above and strolled past 12,13,14,15,16...and 17. The room was lit by a single light bulb casting a circle of electric current on the floor.

He crept in the doorway and stood a few feet before the light. Sebastian was sitting in the middle of the light in a chair, and he was holding a gun. He looked up as he heard Sherlock approaching.

"So you_ have_ returned to London. Interesting. Heard you were in Amsterdam for a while there-almost had you then. And at the monastery and in Germany too-we did set traps for you, when we knew you were on the case. You couldn't resist showing off could you? No, because even when you're supposed to be dead you had to interfere. "

"Well, your certainly very observant Sebastian,and will give you that. But I did escape those traps, you didn't catch me. I am better than you Sebastain,and I will kill you. Maybe not now, but eventually I will." Sherlock smirked.

"Oh, I don't know-it seems to me that whenever you threaten to kill someone, Sherlock, it never exactly turns out the way you want it to. Remember Moriarty,how he found all your weak spots and exploited them? I could do that to you. Again. But what's the fun in that? That's boring and besides, it already has been done. No, I prefer good old fashioned blackmail. As I am sure you do know, I am also a reasonably good sniper. So don't threaten me, not unless you want to suffer."

"So you are working with Charles Augustus Magnussen?"

"That would be telling, wouldn't it? Well, this has been very interesting, but I am a busy man and time is money after all.

"Yes, I suppose you have a whole list of people to go murder" Sherlock snapped.

Sebastian stood up and put his gun over his shoulder. He smirked.

''You'll be seeing me soon Sherlock. Sooner than you may think" He added as a parting remark.

He re-adjusted his gun over his shoulders and walked out the door at a brisk pace.

Sherlock did not try to follow. He knew that the next time he saw Sebastian would be when Sebastian wanted.

He made his way back down the creaky metal steps and out through the gloom of the lower warehouse floor. The door shut behind him with a clang. The street was still dark,but it was lighter out now.

Sherlock went over his options. Sebastian would try to lure him to him-maybe with a murder,maybe something else. Or he could of course just shoot Sherlock from a rooftop and no-one would really ever find out. That would be the simplest,but Sebastian said he wanted it to be different. _Blackmail_ he had said.. He didn't think Sebastian would be so drastic as do something that would alert Scotland Yard,but then again,they were all idiots. Except for Lestrade possibly. After all-crime is common, logic is rare. At least he didn't have much to lose this time he thought grimly. Not as much,no,but still a lot. Lives at stake. And the risk was high.

- Sherlock got awoken by his phone ringing at about 8:30 in the morning almost a week later. He yawned. God, he was tired. He had chased after one of Sebastian's leads in the city last night,and the guy still got away. And then he had stayed up till about 3:00 following other leads. He was getting careless and he knew it. He very groggily got up and went over to his phone. He slid the unlock bar and looked at who the call was from. It was from a number that he hadn't gotten a call from in almost three years. John.

"Sherlock"

"..John,why are you calling?" He pinched the bridge of his nose. If Sebastian found out...

"I-I need to ask you for help Sherlock." He could hear the panick in John's voice. Panick from what?

"It's 8:30 in the morning,clearly whatever you "

"Sherlock please. It's Mary. She's gone." Sherlock sighed. Dammit Sebastian.

"What?"

"How long has she been missing John?"

"About two days,why? I called her today and she didn't answer. Apparently, she went home from work the night before last,didn't return,and her roommate says she hasn't been home since"

"So the probability is that she's missing,correct?''

"Yeah"

"Why would you call me? Why not Scotland Yard?"

John laughed. "Because of what I found on her apartment door. I went over there last night,and I found a note taped on her door. It said...it said "IOU a Death". That's what Moriarty was so focused on wasn't it? IOU? And also,because when the police is out of their depth,which is always,they come to you. And,well..you're my friend Sherlock".

IOU. Sebastian must've known-somehow,someway, He wanted to,contrary to what he said,destroy him like Moriarty wanted to. But it wasn't just him he was destroying. It was John too. He couldn't allow that could he? Never. He'd rather die. He had proved this before though.

"John, what can I do to help?"

"I don't know"

"Well since I don't think there are many leads to go on,I would like to see that paper that you found. "

"Sure yeah,I know a good coffee shop near North Gowers Street"

"Alright"

**Did you like it? Please read/review/fav/follow,it would be appreciated. Thanks! :) **


End file.
